Okay, since this is going to be an independent system, you can do about anything. Here is a few pages from The Homeowner's Guide to Coal Burning Stoves and Furnaces, by James W. Morrison, copyright 1981, ISBN 0668051000. I would recommend either going to the local Library to see if they have a copy, or go to http://www.abebooks.com
to get a copy for yourself. The information is very useful for what you want to do.
If you follow these formulas it will provide a very good system. The sizes are slightly larger than using the ductulator charts used today, but for solid fuel heating the extra duct size provides greater volume and lower duct temperature when using these charts from this book. I prefer to use round piping entirely because it is easier to work with, seals better, and doesn't need specially fabricated, but you can use square or rectangle too, just as long as the square inch area is around the same size you need.
Since this is a new system, I would also think about making your new system a hybrid, forced air and gravity. What I mean by this is that you would size your pipes runs to the needed Btu to your rooms and run the piping on the inside walls of the house, making the leader pipes as short as possible to their register or wall stack. The cold air returns for the blower may be taken from either the outside walls or a centrally located first floor hallway. The cold air return for the gravity side will need to be cut into either one or both sides of your furnace jacket. A motorized spring damper, that is normally open and closes when the furnace blower turns on, will need to be place inline on the gravity side using extra return duct(s) sized generously to your new jacket cutout(s). The reason is you need to seal the jacket back up and pressurize the duct system so the blower doesn't take the easy route through your gravity returns. The purpose of this is to provide you with the advantage of using gravity heat flow when the blower is not running, reducing your blower cycling, while providing you with a safety factor for when you may lose power and don't have it backed up with another power source.
The key to gravity systems is having generous return air flow and no restrictions in the duct and as little as possible bends for the warm air supply. Piping your system like this will be a joy to operate. There is a few diagrams in the U.S.Stove manual on pages 5 and 6 here that show you how to cut out and modify your furnace jacket. It was intended to be used as a series set up, but it will give you a good idea.
This link is broken, either the page no longer exists or there is some other issue like a typo.
Don't expect that the gravity side will work as well or as efficient as the forced air side, but is does work rather well during normal cycle operation. At least you will have heat when the power goes out and you won't run the risk of over firing your new stove. For a gravity system to work well, there needs to be a generous amount of air space in the furnace jacket, but that would not work well with forced air because the air would not wash enough heat off the firebox, unless there is a restrictive plate installed into the furnace bonnet.
The neat thing about gravity heating is that it is quiet, steady, and the height of the wall stacks to the rooms determine their capacity and flow. If at all possible, run the warm air supply registers high in the inside wall. This will cause a chimney effect and draw more air up than if the registers were in the floor. I wouldn't be too concerned about the rise of the warm air supply pipe, they can be run horizontal unless the run is extremely long. Usually 15 to 20 feet is okay run horizontal. Anything over that should have a rise and 24 feet is considered to be the maximum for a gravity warm air leader pipe. The returns for gravity should be short as possible with the least amount of turns in the floor. You can take the return form either inside or outside walls. The returns should at least equal the total amount of square inches of leader pipes. When you cut out the gravity return opening in the jacket, make sure that the hole is wide and no higher than 14 inches. The reason for this is you don't want any heat radiation from the firebox reflecting into the gravity returns. Any heat radiation into a gravity return will reduce the flow through the system by heating the return air into the furnace jacket.
I know this was a little lengthy, but I hope I provided you with enough working knowledge to design yourself a totally awesome fuel efficient warm air heating system.
Feel free to ask away, I'll be watching and ready to help. DOUG